I have several subscriptions organized in a folder. If I ctrl-click on the folder and select Mark All Articles as Read, I see some text in the status bar at the bottom of the window about refreshing subscriptions, but nothing is marked as read.

Additionally, I do have the preference set to mark a selected article as read after a short period, but that does not seem to be working anymore.

I've got the same problem; nothing I do will mark the articles as read. I've tried marking individual articles as well as all articles, but they remain in bold type and showing when filtering in unread articles. This behavior just started a couple of days ago; prior to that reading an article would mark it as read. I'm at version 3.1.9 :e81515b, but I can't remember exactly when I upgraded and if the problem started then..